Listening on http://127.0.0.1:43783 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save saving 'login and webservicepassword' ... In function read_workflowid read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Request started from user roschi Bfabric query: workflow containerid = 3 Warning in bfabricShiny::read(bf$login(), bf$webservicepassword(), posturl = posturl(), : query failed. Warning: Error in $: $ operator is invalid for atomic vectors 121: append 120: [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#125] 104: read_workflowid 97: renderUI [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#135] 96: func 83: renderFunc 82: output$workflow 1: runApp In function read_workflowid Bfabric query: workflow containerid = 32241 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 3606 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3606 workflowtemplate step id 230 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 3606 Selected workflows ids: 3607 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3606 workflowtemplate step id 230 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 3607 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 3606 Selected workflows ids: 3607 Selected workflows ids: 3618 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3606 workflowtemplate step id 230 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 3607 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 3618 workflowtemplate step id 249 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis Selected workflows ids: 3606 Selected workflows ids: 3607 Selected workflows ids: 3618 Selected workflows ids: 3620 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3606 workflowtemplate step id 230 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 3607 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 3618 workflowtemplate step id 249 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis In function read_steptemplateid Bfabric query: workflowstep workflowid = 3620 workflowtemplate step id 256 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 3606 workflowtemplate step id 230 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3607 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3618 workflowtemplate step id 249 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3620 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md ! Undefined control sequence. l.152 (Thermo).\n Inclusion list: Warning: Error in : LaTeX failed to compile /tmp/RtmpTWNsXd/fgcz_order_report-32241.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See fgcz_order_report-32241.log for more info. 157: stop 156: show_latex_error 155: on_error 153: run_engine 152: latexmk_emu 151: tinytex::latexmk 150: latexmk 149: rmarkdown::render 148: eventReactiveValueFunc [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#330] 104: report 97: renderUI [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#343] 96: func 83: renderFunc 82: output$downloadReportButton 1: runApp generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 3606 workflowtemplate step id 230 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3607 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3618 workflowtemplate step id 249 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3620 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-32241.pdf bfabricUpload generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 3606 workflowtemplate step id 230 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3607 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3618 workflowtemplate step id 249 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3620 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-32241.pdf bfabricUpload Execution halted